Coral tissues were removed from the skeleton using an airbrush filled with double‐distilled water (ddH2O) and attached to a compressed air cylinder. To obtain enough tissue for AA‐CSIA, the three replicate coral ramets within each treatment tank were pooled to produce a single coral blastate for each genet within a treatment (n = 2 genets per treatment). The isolated tissue blastate was kept on ice, briefly homogenized, and filtered through 20‐μm mesh to remove skeletal debris (Wall et al. 2020 ). Host and symbiont tissues were separated by repeated centrifugation and ddH2O rinses (Muscatine et al. 1989 ), and isolated tissues were lyophilized and stored at room temperature until analyzed. Isotopic values are reported in delta values (δ) using per mill (‰) notation relative to standard materials (Vienna Pee‐Dee Belemnite [V‐PDB] and atmospheric N2 standards [Air] for carbon and nitrogen, respectively). Samples for bulk tissue carbon (δ13C) and nitrogen (δ15N) isotope analyses and C : N ratios for coral host, symbiont algae and plankton tissues (ca. 1 mg) were packed in tin capsules and measured on a Costech elemental combustion system coupled to a Thermo‐Finnigan Delta Plus XP isotope ratio mass spectrometer. Sample analytical accuracy and precision (δ13C and δ15N) was <0.2‰ (see Supporting Information Appendix S1).
Deltaplus xp isotope ratio mass spectrometer
Manufactured by Thermo Fisher Scientific
Sourced in Germany
The DeltaPlus XP is an isotope ratio mass spectrometer manufactured by Thermo Fisher Scientific. It is designed to measure the relative abundance of stable isotopes in a sample with high precision.
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Lab products found in correlation
Flash ea 1112 series elemental analyser, by Thermo Fisher Scientific (3 mentions)
Conflo 3, by Thermo Fisher Scientific (1 mentions)
Agilent 5973, by Agilent Technologies (1 mentions)
Agilent 7697a, by Agilent Technologies (1 mentions)
Delta 5 advantage irms, by Thermo Fisher Scientific (1 mentions)
Prominence hplc system, by Shimadzu (1 mentions)
Vario pyro cube, by Elementar (1 mentions)
7 protocols using deltaplus xp isotope ratio mass spectrometer
1
Coral Tissue Preparation for Isotopic Analysis
2
Soil Invertebrate Trophic Analysis
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Individuals were counted and identified under a dissecting microscope to order and trophic group for Collembola74 and Acari75 . Other invertebrates were separated according to taxa and trophic group. The biomass of each order/taxa was estimated by measuring the average body length (mm) per field, using the formula by Caruso and Migliorini76 (link) for the mites and by Ganihar77 for the other orders. The samples were further grouped into 7 main trophic groups in order to have sufficient material to analyse 13C and 15N: detritivorous Collembola, detritivorous mites (oribatid, astigmata and prostigmata mites), annelids, other detritivorous (detritivorous coleoptera, myriapoda and diptera larvae), herbivores (hemiptera and thysanoptera) predaceous mites (mesostigmata and predaceous prostigmata) and predaceous fauna (arachnida, chilopoda, predatory coleoptera and symphyla) (Fig. 1 ). Each of these groups was transferred into a tin capsule in 70% ethanol, oven-dried and weighed prior to analysis. All the samples were analysed for total C and N content and δ13C and δ15N using a Flash EA 1112 Series Elemental Analyser connected via a Conflo III to a DeltaPlus XP isotope ratio mass spectrometer (Thermo Finnigan, Bremen, Germany).
3
Soil Carbon, Nitrogen, and Phosphorus in Scottish Peat
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The National Soil Inventory of Scotland (NSIS2) (Lilly et al., 2011) contains 721 soil profiles sampled between 2007 and 2009 for which C, N, and P concentrations have been measured. Here we consider ten of these sites, those classified as deep blanket peat. Details for all methods are given in Chapman et al. (2013) . In brief, the selected peat profiles were 90-120 cm in thickness and samples taken at between three and five depths, often based on observed changes in humification in the peat profile. Bulk density was measured in triplicate on subsamples collected in 7.3 cm internal diameter stainless steel cylinders, adjusted to correct for removal of the N2 mm fraction. Around 2 kg of sample were taken at each site for elemental analysis, returned to the laboratory where they were air-dried at 30 °C and sieved (b 2 mm), further dried at 50 °C prior to milling. Carbon and nitrogen were determined using a Flash EA 1112 Series Elemental Analyser connected via a Conflo III to a DeltaPlus XPisotope ratio mass spectrometer (all Thermo Finnigan, Bremen, Germany). The C contents were calculated from the area output of the mass spectrometer calibrated against a standard reference material which was analysed with every batch of ten samples). Total P was measured colorimetrically following fusion with NaOH (Smith and Bain, 1982) .
4
Soil Invertebrate Community Analysis
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Individuals were counted and identified under a dissecting microscope to order and trophic group for Collembola 36 and Acari 37 . Other invertebrates were separated according to taxa and trophic group. The biomass of each order/taxa was estimated by measuring the average body length (mm) per field, using the formula by Caruso and Migliorini 38 for the mites and by
Ganihar 39 for the other orders. The samples were further grouped into 7 main trophic groups in order to have sufficient material to analyse 13 C and 15 N: detritivorous Collembola, detritivorous mites (oribatid, astigmata and prostigmata mites), annelids, other detritivorous (detritivorous coleoptera, myriapoda and diptera larvae), herbivores (hemiptera and thysanoptera) predaceous mites (mesostigmata and predaceous prostigmata) and predaceous fauna (arachnida, chilopoda, predatory coleoptera and symphyla). Each of these groups was transferred into a tin capsule in 70 % ethanol, oven-dried and weighed prior to analysis. All the samples were analysed for total C and N content and δ 13 C and δ 15 N using a Flash EA 1112
Series Elemental Analyser connected via a Conflo III to a DeltaPlus XP isotope ratio mass spectrometer (Thermo Finnigan, Bremen, Germany).
Ganihar 39 for the other orders. The samples were further grouped into 7 main trophic groups in order to have sufficient material to analyse 13 C and 15 N: detritivorous Collembola, detritivorous mites (oribatid, astigmata and prostigmata mites), annelids, other detritivorous (detritivorous coleoptera, myriapoda and diptera larvae), herbivores (hemiptera and thysanoptera) predaceous mites (mesostigmata and predaceous prostigmata) and predaceous fauna (arachnida, chilopoda, predatory coleoptera and symphyla). Each of these groups was transferred into a tin capsule in 70 % ethanol, oven-dried and weighed prior to analysis. All the samples were analysed for total C and N content and δ 13 C and δ 15 N using a Flash EA 1112
Series Elemental Analyser connected via a Conflo III to a DeltaPlus XP isotope ratio mass spectrometer (Thermo Finnigan, Bremen, Germany).
5
Leaf dark-respired CO2 sampling protocol
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Leaf dark-respired CO2 was sampled at the above-listed time points using the in-tube incubation method originally described by Werner et al. (2007) (link) and modified by Lehmann et al. (2015) (link). In short, leaf material was placed in 12 ml gas-tight glass vials (‘Exetainer’, Labco Ltd, Lampeter, Ceredigion, UK) and flushed with CO2-free synthetic air (Pangas, Dagmersellen, Switzerland). The exetainer was immediately darkened for 4 min, and subsequently an aliquot of the sample air (now with respired CO2) was transferred with a gas-tight syringe into a second exetainer pre-filled with dry N2 (N2 5.0, Pangas). In addition, climate chamber air samples were taken and transferred to N2-filled exetainers. The gaseous samples in the exetainers were then analyzed using a modified Gasbench II (Zeeman et al., 2008 (link)) connected to a DeltaPlusXP isotope ratio mass spectrometer (Thermo-Fisher, Bremen, Germany) with a precision of ~0.1‰ (SD) for a quality control standard (400 ppm CO2 in artificial air).
6
Analyzing Methane and Dissolved Carbon Isotopes
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The stable carbon isotope ratios of methane were measured using a Finnigan DELTA plus XP isotope-ratio mass spectrometer (IR-MS) equipped with a Hewlett Packard 5890 gas chromatograph (GC) and a ThermoQuest combustion interface (Thermo Fisher Scientific, Waltham, MA, USA). The dissolved inorganic carbon (DIC) was measured using a DELTA V Advantage IR-MS equipped with a gas chromatography-based GasBench II system (Thermo Fisher Scientific).
The porewater was squeezed from the subcore samples using an automatic hydraulic press (AUTOFOUR/30: Carver, Inc., Summit, NJ). After the water chemistry was measured on board, the water samples were stored at −80 °C until further processing in the laboratory. The acetate concentration in the porewater sample was measured using a Prominence HPLC system (Shimadzu Co. Ltd., Kyoto, Japan) equipped with an electrical conductivity detector. The concentrations of methylated compounds, methanol, dimethyl sulfide and trimethylamine (TMA) in the porewater sample were measured using GC/MS (Agilent 5973, Agilent Technologies, Santa Clara, CA, USA) equipped with a headspace sampler (Agilent 7697A, Agilent Technologies).
The porewater was squeezed from the subcore samples using an automatic hydraulic press (AUTOFOUR/30: Carver, Inc., Summit, NJ). After the water chemistry was measured on board, the water samples were stored at −80 °C until further processing in the laboratory. The acetate concentration in the porewater sample was measured using a Prominence HPLC system (Shimadzu Co. Ltd., Kyoto, Japan) equipped with an electrical conductivity detector. The concentrations of methylated compounds, methanol, dimethyl sulfide and trimethylamine (TMA) in the porewater sample were measured using GC/MS (Agilent 5973, Agilent Technologies, Santa Clara, CA, USA) equipped with a headspace sampler (Agilent 7697A, Agilent Technologies).
7
Oxygen Isotope Analysis of Stem Xylem Water and Needle Assimilates
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The δ 18 O of cryogenically extracted stem xylem water, as a proxy for source water, was analyzed using a thermal combustion/elementary analysis (TC/EA) system coupled to a DeltaPlusXP isotope ratio mass spectrometer (IRMS; all supplied by Thermo Fisher Scientific, Bremen, Germany) with a typical measurement precision (SD) of 0.2%•.
For the extraction of assimilates, a total of 60 mg ground needle material was transferred to a 2 mL reaction tube, dissolved in 1.5 mL of hot (85 • C) water and heated in a water bath at 85 • C for 30 min (Lehmann et al. 2017) . Subsequently, samples were cooled down at room temperature and centrifuged (2 min, 10,000g), and the supernatant containing the water-soluble compounds (WSC) was transferred to a new reaction vial. An aliquot (ca. 0.6 mg) of the WSC, as a proxy for assimilates, was transferred to silver capsules, frozen at -20 • C and freezedried. Carbon (δ 13 C, VPDB) and oxygen (δ 18 O, VSMOW) isotope ratios were measured using a TC/EA system (vario PYRO cube, Elementar, Hanau, Germany) coupled to the abovementioned IRMS. The typical measurement precision (SD) was 0.3%• for δ 13 C values and 0.2%• for δ 18 O values. The 18 O enrichment of needle assimilates ( 18 O WSC ) above source water was calculated as the difference between the δ 18 O of WSC and the δ 18 O of the stem xylem water (source water) in the same tree at the same date.
For the extraction of assimilates, a total of 60 mg ground needle material was transferred to a 2 mL reaction tube, dissolved in 1.5 mL of hot (85 • C) water and heated in a water bath at 85 • C for 30 min (Lehmann et al. 2017) . Subsequently, samples were cooled down at room temperature and centrifuged (2 min, 10,000g), and the supernatant containing the water-soluble compounds (WSC) was transferred to a new reaction vial. An aliquot (ca. 0.6 mg) of the WSC, as a proxy for assimilates, was transferred to silver capsules, frozen at -20 • C and freezedried. Carbon (δ 13 C, VPDB) and oxygen (δ 18 O, VSMOW) isotope ratios were measured using a TC/EA system (vario PYRO cube, Elementar, Hanau, Germany) coupled to the abovementioned IRMS. The typical measurement precision (SD) was 0.3%• for δ 13 C values and 0.2%• for δ 18 O values. The 18 O enrichment of needle assimilates ( 18 O WSC ) above source water was calculated as the difference between the δ 18 O of WSC and the δ 18 O of the stem xylem water (source water) in the same tree at the same date.
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